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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object charite.christo.protein.ProteinWriter1
public class ProteinWriter1
Write a protein file
Field Summary |
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Fields inherited from interface charite.christo.protein.ProteinWriter |
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ATOM_LINES, CHAIN_A, CHAIN_B, CHAIN_SPACE, COMPLETE_PDB, FASTA, HELIX_SHEET, HETEROS, IDX_FOR_RESNUM, MET_INSTEAD_OF_MSE, NUCLEOTIDE_STRUCTURE, NUCLEOTIDES, PDB, SEQRES, SEQRES_IF_COORDINATES, SIDE_CHAIN_ATOMS |
Constructor Summary | |
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ProteinWriter1()
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Method Summary | |
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static java.lang.String |
createPairfitTarget(Protein p,
Matrix3D m,
BA ba)
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java.lang.String |
getFileSuffix()
Extension ".pdb" forPDB-files and ".fa" for fasta-files |
static BA |
mergePdbWithOriginal(Protein p)
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void |
selectResidues(boolean[] isSelected)
do not write all residues but only a certain subset. |
void |
setResidueRange(int from,
int to)
index of first and last amino acid |
boolean |
toText(Protein p,
Matrix3D[] mm3d,
long options,
BA sb)
Writes the protein data e.g. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinWriter1()
Method Detail |
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public void selectResidues(boolean[] isSelected)
selectResidues
in interface ProteinWriter
public java.lang.String getFileSuffix()
ProteinWriter
getFileSuffix
in interface ProteinWriter
public void setResidueRange(int from, int to)
ProteinWriter
setResidueRange
in interface ProteinWriter
public boolean toText(Protein p, Matrix3D[] mm3d, long options, BA sb)
ProteinWriter
toText
in interface ProteinWriter
public static final java.lang.String createPairfitTarget(Protein p, Matrix3D m, BA ba)
public static final BA mergePdbWithOriginal(Protein p)
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